1VKZ - JenaLib

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Title :   CRYSTAL STRUCTURE OF PHOSPHORIBOSYLAMINE--GLYCINE LIGASE (TM1250) FROM THERMOTOGA MARITIMA AT 2.30 A RESOLUTION

Authors :   Joint Center For Structural Genomics (Jcsg)

Date :   29 Jun 04 (Deposition) - 24 Aug 04 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)

Keywords :   Tm1250, Phosphoribosylamine--Glycine Ligase, Structural Genomics, Jcsg, Protein Structure Initiative, Psi, Joint Center For Structural Genomics, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Phosphoribosylamine--Glycine Ligase (Tm1250) From Thermotoga Maritima At 2. 30 A Resolution
To Be Published
PubMed: search

Molecule 1 - PHOSPHORIBOSYLAMINE--GLYCINE LIGASE
	Chains	:	A, B
	EC Number	:	6.3.4.13
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	PURD, TM1250
	Mutation	:	YES
	Organism Scientific	:	THERMOTOGA MARITIMA
	Organism Taxid	:	2336
	Synonym	:	GARS, GLYCINAMIDE RIBONUCLEOTIDE SYNTHETASE, PHOSPHORIBOSYLGLYCINAMIDE SYNTHETASE

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 15)

No.	Name	Count	Type	Full Name
1	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
2	MSE	14	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (1, 7)

No.	Name	Count	Type	Full Name
1	EDO	-1	Ligand/Ion	1,2-ETHANEDIOL
2	MSE	7	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 2 (2, 8)

No.	Name	Count	Type	Full Name
1	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
2	MSE	7	Mod. Amino Acid	SELENOMETHIONINE

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LEU B:180	BINDING SITE FOR RESIDUE EDO B 401

(no "SS Bond" information available for 1VKZ)

Asymmetric Unit

No.	Residues
1	Tyr A:32	-	Pro A:33
2	Gly A:224	-	Pro A:225
3	Asp A:280	-	Pro A:281
4	Tyr A:326	-	Pro A:327
5	Tyr B:32	-	Pro B:33
6	Gly B:224	-	Pro B:225
7	Asp B:280	-	Pro B:281
8	Tyr B:326	-	Pro B:327

(no "SAP(SNP)/Variant" information available for 1VKZ)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GARS	PS00184	Phosphoribosylglycinamide synthetase signature.	PUR2_THEMA	277-284	2	A:277-284 B:277-284

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GARS	PS00184	Phosphoribosylglycinamide synthetase signature.	PUR2_THEMA	277-284	1	A:277-284 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GARS	PS00184	Phosphoribosylglycinamide synthetase signature.	PUR2_THEMA	277-284	1	- B:277-284

(no "Exon" information available for 1VKZ)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:391
 aligned with PUR2_THEMA | Q9X0X7 from UniProtKB/Swiss-Prot  Length:400

    Alignment length:396
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393      
           PUR2_THEMA     4 VRVHILGSGGREHAIGWAFAKQGYEVHFYPGNAGTKRDGTNHPYEGEKTLKAIPEEDIVIPGSEEFLVEGVSNWRSNVFGPVKEVARLEGSKVYAKRFMKKYGIRTARFEVAETPEELREKIKKFSPPYVIKADGLARGKGVLILDSKEETIEKGSKLIIGELIKGVKGPVVIDEFLAGNELSAMAVVNGRNFVILPFVRDYKRLMDGDRGPNTGGMGSWGPVEIPSDTIKKIEELFDKTLWGVEKEGYAYRGFLYLGLMLHDGDPYILEYNVRLGDPETEVIVTLNPEGFVNAVLEGYRGGKMEPVEPRGFAVDVVLAARGYPDAPEKGKEITLPEEGLIFFAGVAEKDGKLVTNGGRVLHCMGTGETKEEARRKAYELAEKVHFEGKTYRRDIA 399
               SCOP domains d1vkza2 A:4-93 Glycinamide ribonucleotide synthetase (GAR-syn), N-dom     ain             d1vkza3 A:94-313 Glycinamide ribonucleotide synthetase (GAR-syn), domain 2                                                                                                                                                  d1vkza1 A:314-399 Glycinamide ribonucleotide synthetase (GAR-syn), C-domain            SCOP domains
               CATH domains 1vkzA01 A:4-85  [code=3.40.50.20, no name defined]                                -------------------------1vkzA02 A:111-180 ATP-grasp fold, A domain                            1vkzA03 A:181-314 ATP-grasp fold, B domain                                                                                            1vkzA04 A:315-399 Glycinamide Ribonucleotide Synthetase; Chain A, domain 4            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeee.hhhhhhhhhhhhhh..eeeeee...hhhhh.ee....hhhhhhh.....ee...hhhhh..-----.......hhhhhhhhhhhhhhhhhhhhh......eeee.hhhhhhhhhh.....eeeee........eeee.hhhhhhhhhhhhhh..........eeeee....eeeeeeeeee..eeee....ee..eee...eeee....eeee....hhhhhhhhhhhhhhhhhhhhhh....eeeeeeeeeee..eeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhh..........eeeeeeee.....................eee..eeee..eeee...eeeeeeeee.hhhhhhhhhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GARS    ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1vkz A   4 VRVHILGSGGREHAIGWAFAKQGYEVHFYPGNAGTKRDGTNHPYEGEKTLKAIPEEDIVIPGSEEFLVE-----RSNVFGPVKEVARLEGSKVYAKRFmKKYGIRTARFEVAETPEELREKIKKFSPPYVIKADGLARGKGVLILDSKEETIEKGSKLIIGELIKGVKGPVVIDEFLAGNELSAmAVVNGRNFVILPFVRDYKRLmDGDRGPNTGGmGSWGPVEIPSDTIKKIEELFDKTLWGVEKEGYAYRGFLYLGLmLHDGDPYILEYNVRLGDPETEVIVTLNPEGFVNAVLEGYRGGKmEPVEPRGFAVDVVLAARGYPDAPEKGKEITLPEEGLIFFAGVAEKDGKLVTNGGRVLHCmGTGETKEEARRKAYELAEKVHFEGKTYRRDIA 399
                                    13        23        33        43        53        63        |-    |   83        93       103       113       123       133       143       153       163       173       183    |  193       203     | 213      |223       233       243       253       263       273       283       293       303   |   313       323       333       343       353       363   |   373       383       393      
                                                                                               72    78                     102-MSE                                                                               188-MSE              209-MSE    220-MSE                                    263-MSE                                     307-MSE                                                     367-MSE

Chain B from PDB  Type:PROTEIN  Length:391
 aligned with PUR2_THEMA | Q9X0X7 from UniProtKB/Swiss-Prot  Length:400

    Alignment length:396
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393      
           PUR2_THEMA     4 VRVHILGSGGREHAIGWAFAKQGYEVHFYPGNAGTKRDGTNHPYEGEKTLKAIPEEDIVIPGSEEFLVEGVSNWRSNVFGPVKEVARLEGSKVYAKRFMKKYGIRTARFEVAETPEELREKIKKFSPPYVIKADGLARGKGVLILDSKEETIEKGSKLIIGELIKGVKGPVVIDEFLAGNELSAMAVVNGRNFVILPFVRDYKRLMDGDRGPNTGGMGSWGPVEIPSDTIKKIEELFDKTLWGVEKEGYAYRGFLYLGLMLHDGDPYILEYNVRLGDPETEVIVTLNPEGFVNAVLEGYRGGKMEPVEPRGFAVDVVLAARGYPDAPEKGKEITLPEEGLIFFAGVAEKDGKLVTNGGRVLHCMGTGETKEEARRKAYELAEKVHFEGKTYRRDIA 399
               SCOP domains d1vkzb2 B:4-93 Glycinamide ribonucleotide synthetase (GAR-syn), N-dom     ain             d1vkzb3 B:94-313 Glycinamide ribonucleotide synthetase (GAR-syn), domain 2                                                                                                                                                  d1vkzb1 B:314-399 Glycinamide ribonucleotide synthetase (GAR-syn), C-domain            SCOP domains
               CATH domains 1vkzB01 B:4-85  [code=3.40.50.20, no name defined]                                -------------------------1vkzB02 B:111-180 ATP-grasp fold, A domain                            1vkzB03 B:181-314 ATP-grasp fold, B domain                                                                                            1vkzB04 B:315-399 Glycinamide Ribonucleotide Synthetase; Chain A, domain 4            CATH domains
           Pfam domains (1) GARS_N-1vkzB05 B:4-92                                                                    GARS_A-1vkzB01 B:93-283                                                                                                                                                                        -------------------------------GARS_C-1vkzB03 B:315-399                                                              Pfam domains (1)
           Pfam domains (2) GARS_N-1vkzB06 B:4-92                                                                    GARS_A-1vkzB02 B:93-283                                                                                                                                                                        -------------------------------GARS_C-1vkzB04 B:315-399                                                              Pfam domains (2)
         Sec.struct. author .eeeeee.hhhhhhhhhhhhhh..eeeeee...hhhhh.ee....hhhhhhh.....ee...hhhhh..-----.......hhhhhhhhhhhhhhhhhhhhh......eeee.hhhhhhhhhh.....eeeee........eeee.hhhhhhhhhhhhhh..........eeeee....eeeeeeeeee..eeee....ee..eee...eeee....eeee....hhhhhhhhhhhhhhhhhhhhhh....eeeeeeeeeee..eeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhh..........eeeeeeee.....................eee..eeee..eeee...eeeeeeeee.hhhhhhhhhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GARS    ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1vkz B   4 VRVHILGSGGREHAIGWAFAKQGYEVHFYPGNAGTKRDGTNHPYEGEKTLKAIPEEDIVIPGSEEFLVE-----RSNVFGPVKEVARLEGSKVYAKRFmKKYGIRTARFEVAETPEELREKIKKFSPPYVIKADGLARGKGVLILDSKEETIEKGSKLIIGELIKGVKGPVVIDEFLAGNELSAmAVVNGRNFVILPFVRDYKRLmDGDRGPNTGGmGSWGPVEIPSDTIKKIEELFDKTLWGVEKEGYAYRGFLYLGLmLHDGDPYILEYNVRLGDPETEVIVTLNPEGFVNAVLEGYRGGKmEPVEPRGFAVDVVLAARGYPDAPEKGKEITLPEEGLIFFAGVAEKDGKLVTNGGRVLHCmGTGETKEEARRKAYELAEKVHFEGKTYRRDIA 399
                                    13        23        33        43        53        63        |-    |   83        93       103       113       123       133       143       153       163       173       183    |  193       203     | 213      |223       233       243       253       263       273       283       293       303   |   313       323       333       343       353       363   |   373       383       393      
                                                                                               72    78                     102-MSE                                                                               188-MSE              209-MSE    220-MSE                                    263-MSE                                     307-MSE                                                     367-MSE

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: ATP-grasp (83)

Family: GARS_A (12)

Thermotoga maritima (1)

1a	GARS_A-1vkzB01	B:93-283
1b	GARS_A-1vkzB02	B:93-283

Clan: no clan defined [family: GARS_C] (12)

Family: GARS_C (12)

Thermotoga maritima (1)

2a	GARS_C-1vkzB03	B:315-399
2b	GARS_C-1vkzB04	B:315-399

Clan: no clan defined [family: GARS_N] (12)

Family: GARS_N (12)

Thermotoga maritima (1)

3a	GARS_N-1vkzB05	B:4-92
3b	GARS_N-1vkzB06	B:4-92

Asymmetric Unit(hide GO term definitions)

Chain A,B (PUR2_THEMA | Q9X0X7)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	GO:0016874	ligase activity	Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
	GO:0000287	magnesium ion binding	Interacting selectively and non-covalently with magnesium (Mg) ions.
	GO:0030145	manganese ion binding	Interacting selectively and non-covalently with manganese (Mn) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	GO:0004637	phosphoribosylamine-glycine ligase activity	Catalysis of the reaction: 5-phospho-D-ribosylamine + ATP + glycine = N(1)-(5-phospho-D-ribosyl)glycinamide + ADP + 2 H(+) + phosphate.
biological process
	GO:0006189	'de novo' IMP biosynthetic process	The chemical reactions and pathways resulting in the formation of IMP, inosine monophosphate, by the stepwise assembly of a purine ring on ribose 5-phosphate.
	GO:0009113	purine nucleobase biosynthetic process	The chemical reactions and pathways resulting in the formation of purine nucleobases, one of the two classes of nitrogen-containing ring compounds found in DNA and RNA, which include adenine and guanine.
	GO:0006164	purine nucleotide biosynthetic process	The chemical reactions and pathways resulting in the formation of a purine nucleotide, a compound consisting of nucleoside (a purine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.

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	Cis Peptide Bonds
		Asp A:280 - Pro A:281	[ RasMol ]
		Asp B:280 - Pro B:281	[ RasMol ]
		Gly A:224 - Pro A:225	[ RasMol ]
		Gly B:224 - Pro B:225	[ RasMol ]
		Tyr A:32 - Pro A:33	[ RasMol ]
		Tyr A:326 - Pro A:327	[ RasMol ]
		Tyr B:32 - Pro B:33	[ RasMol ]
		Tyr B:326 - Pro B:327	[ RasMol ]

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Description

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Ligands, Modified Residues, Ions (2, 15)

Sites (1, 1)

SS Bonds (0, 0)

Cis Peptide Bonds (8, 8)

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